How to remove ambiguities? about seqtk HOT 4 OPEN

Something like this Perl one-liner:

perl -pe 's/[^AGTC]/N/gi unless m/>/;'  old.fa > new.fa

If a line has a > leave it alone, otherwise replace all non-AGTC characters with N.

The -p option puts an implicit "read + print lines" loop around the file.

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@MrOlm good point! Can also use sed:

% cat seq.fa

>good
AGTCTCTTC
>bad
AGRGAATNC

% sed '/^[^>]/ s/[^AGTC]/N/gi' < seq.fa

>good
AGTCTCTTC
>bad
AGNGAATNC

from seqtk.

Unfortunately, seqtk doesn't have this functionality. Perhaps it is best to write a script to do this.

from seqtk.

Just a note to the above comment- that perl script also replaces newline characters with Ns. The following small modification seems to fix that:

perl -pe 's/[^AGTC\n]/N/gi unless m/>/;' old.fa > new.fa

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